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. 1985 Jun;82(11):3582–3585. doi: 10.1073/pnas.82.11.3582

Three-dimensional structure of ubiquitin at 2.8 A resolution.

S Vijay-Kumar, C E Bugg, K D Wilkinson, W J Cook
PMCID: PMC397829  PMID: 2987935

Abstract

The three-dimensional structure of ubiquitin has been determined at 2.8 A resolution. X-ray diffraction data for the native protein and derivatives were collected with an automated diffractometer. Phases were obtained by use of a single isomorphous mercuric acetate derivative. The molecule contains a pronounced hydrophobic core. Prominent secondary structural features include three and one-half turns of alpha-helix, a mixed beta-sheet that contains four strands, and seven reverse turns. The histidine, tyrosine, and two phenylalanine residues are located on the surface of the molecule.

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Selected References

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  1. Busch H., Goldknopf I. L. Ubiquitin - protein conjugates. Mol Cell Biochem. 1981 Nov 13;40(3):173–187. doi: 10.1007/BF00224611. [DOI] [PubMed] [Google Scholar]
  2. Cary P. D., King D. S., Crane-Robinson C., Bradbury E. M., Rabbani A., Goodwin G. H., Johns E. W. Structural studies on two high-mobility-group proteins from calf thymus, HMG-14 and HMG-20 (ubiquitin), and their interaction with DNA. Eur J Biochem. 1980 Dec;112(3):577–580. doi: 10.1111/j.1432-1033.1980.tb06123.x. [DOI] [PubMed] [Google Scholar]
  3. Chin D. T., Kuehl L., Rechsteiner M. Conjugation of ubiquitin to denatured hemoglobin is proportional to the rate of hemoglobin degradation in HeLa cells. Proc Natl Acad Sci U S A. 1982 Oct;79(19):5857–5861. doi: 10.1073/pnas.79.19.5857. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Ciechanover A., Finley D., Varshavsky A. The ubiquitin-mediated proteolytic pathway and mechanisms of energy-dependent intracellular protein degradation. J Cell Biochem. 1984;24(1):27–53. doi: 10.1002/jcb.240240104. [DOI] [PubMed] [Google Scholar]
  5. Ciechanover A., Finley D., Varshavsky A. Ubiquitin dependence of selective protein degradation demonstrated in the mammalian cell cycle mutant ts85. Cell. 1984 May;37(1):57–66. doi: 10.1016/0092-8674(84)90300-3. [DOI] [PubMed] [Google Scholar]
  6. Cook W. J., Suddath F. L., Bugg C. E., Goldstein G. Crystallization and preliminary x-ray investigation of ubiquitin, a non-histone chromosomal protein. J Mol Biol. 1979 May 25;130(3):353–355. doi: 10.1016/0022-2836(79)90546-1. [DOI] [PubMed] [Google Scholar]
  7. Finley D., Ciechanover A., Varshavsky A. Thermolability of ubiquitin-activating enzyme from the mammalian cell cycle mutant ts85. Cell. 1984 May;37(1):43–55. doi: 10.1016/0092-8674(84)90299-x. [DOI] [PubMed] [Google Scholar]
  8. Gavilanes J. G., Gonzalez de Buitrago G., Perez-Castells R., Rodriguez R. Isolation, characterization, and amino acid sequence of a ubiquitin-like protein from insect eggs. J Biol Chem. 1982 Sep 10;257(17):10267–10270. [PubMed] [Google Scholar]
  9. Goldknopf I. L., Busch H. N-Bromosuccinimide fragments of protein A24 (uH2A): an implication that ubiquitin is the precursor of conjugation in vivo. Biochem Biophys Res Commun. 1980 Oct 31;96(4):1724–1731. doi: 10.1016/0006-291x(80)91373-x. [DOI] [PubMed] [Google Scholar]
  10. Goldstein G., Scheid M., Hammerling U., Schlesinger D. H., Niall H. D., Boyse E. A. Isolation of a polypeptide that has lymphocyte-differentiating properties and is probably represented universally in living cells. Proc Natl Acad Sci U S A. 1975 Jan;72(1):11–15. doi: 10.1073/pnas.72.1.11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hershko A., Ciechanover A. Mechanisms of intracellular protein breakdown. Annu Rev Biochem. 1982;51:335–364. doi: 10.1146/annurev.bi.51.070182.002003. [DOI] [PubMed] [Google Scholar]
  12. Hershko A., Eytan E., Ciechanover A., Haas A. L. Immunochemical analysis of the turnover of ubiquitin-protein conjugates in intact cells. Relationship to the breakdown of abnormal proteins. J Biol Chem. 1982 Dec 10;257(23):13964–13970. [PubMed] [Google Scholar]
  13. Hunt L. T., Dayhoff M. O. Amino-terminal sequence identity of ubiquitin and the nonhistone component of nuclear protein A24. Biochem Biophys Res Commun. 1977 Jan 24;74(2):650–655. doi: 10.1016/0006-291x(77)90352-7. [DOI] [PubMed] [Google Scholar]
  14. Jenson J., Goldstein G., Breslow E. Physical-chemical properties of ubiquitin. Biochim Biophys Acta. 1980 Aug 21;624(2):378–385. doi: 10.1016/0005-2795(80)90079-3. [DOI] [PubMed] [Google Scholar]
  15. Kagan W. A., O'Neill G. J., Incefy G. S., Goldstein G., Good R. A. Induction of human granulocyte differentiation in vitro by ubiquitin and thymopoietin. Blood. 1977 Aug;50(2):275–288. [PubMed] [Google Scholar]
  16. Kagan W. A., Siegal F. P., Gupta S., Goldstein G., Good R. A. Early stages of human marrow lymphocyte differentiation: induction in vitro by thymopoietin and ubiquitin. J Immunol. 1979 Feb;122(2):686–691. [PubMed] [Google Scholar]
  17. Lehman W. Hybrid troponin reconstituted from vertebrate and arthropod subunits. Nature. 1975 May 29;255(5507):424–426. doi: 10.1038/255424a0. [DOI] [PubMed] [Google Scholar]
  18. Lenkinski R. E., Chen D. M., Glickson J. D., Goldstein G. Nuclear magnetic resonance studies of the denaturation of ubiquitin. Biochim Biophys Acta. 1977 Sep 27;494(1):126–130. doi: 10.1016/0005-2795(77)90140-4. [DOI] [PubMed] [Google Scholar]
  19. Lesk A. M., Hardman K. D. Computer-generated schematic diagrams of protein structures. Science. 1982 Apr 30;216(4545):539–540. doi: 10.1126/science.7071602. [DOI] [PubMed] [Google Scholar]
  20. Levinger L., Varshavsky A. Selective arrangement of ubiquitinated and D1 protein-containing nucleosomes within the Drosophila genome. Cell. 1982 Feb;28(2):375–385. doi: 10.1016/0092-8674(82)90355-5. [DOI] [PubMed] [Google Scholar]
  21. Low T. L., Goldstein A. L. The chemistry and biology of thymosin. II. Amino acid sequence analysis of thymosin alpha1 and polypeptide beta1. J Biol Chem. 1979 Feb 10;254(3):987–995. [PubMed] [Google Scholar]
  22. Low T. L., Thurman G. B., McAdoo M., McClure J., Rossio J. L., Naylor P. H., Goldstein A. L. The chemistry and biology of thymosin. I. Isolation, characterization, and biological activities of thymosin alpha1 and polypeptide beta1 from calf thymus. J Biol Chem. 1979 Feb 10;254(3):981–986. [PubMed] [Google Scholar]
  23. Schlesinger D. H., Goldstein G., Niall H. D. The complete amino acid sequence of ubiquitin, an adenylate cyclase stimulating polypeptide probably universal in living cells. Biochemistry. 1975 May 20;14(10):2214–2218. doi: 10.1021/bi00681a026. [DOI] [PubMed] [Google Scholar]
  24. Watson D. C., Levy W. B., Dixon G. H. Free ubiquitin is a non-histone protein of trout testis chromatin. Nature. 1978 Nov 9;276(5684):196–198. doi: 10.1038/276196a0. [DOI] [PubMed] [Google Scholar]
  25. West M. H., Bonner W. M. Histone 2A, a heteromorphous family of eight protein species. Biochemistry. 1980 Jul 8;19(14):3238–3245. doi: 10.1021/bi00555a022. [DOI] [PubMed] [Google Scholar]
  26. West M. H., Bonner W. M. Histone 2B can be modified by the attachment of ubiquitin. Nucleic Acids Res. 1980 Oct 24;8(20):4671–4680. doi: 10.1093/nar/8.20.4671. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Wilkinson K. D., Audhya T. K. Stimulation of ATP-dependent proteolysis requires ubiquitin with the COOH-terminal sequence Arg-Gly-Gly. J Biol Chem. 1981 Sep 10;256(17):9235–9241. [PubMed] [Google Scholar]

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